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February 2014 Bioinformatics Papers of Note


Berry CC1, Bushman FD, et al.
Comparing DNA integration site clusters with scan statistics.
Bioinformatics. 2014 Feb 14. [Epub ahead of print]

Carin L, Lucas J, et al.
Bayesian joint analysis of heterogeneous genomics data.
Bioinformatics. 2014 Feb 21. [Epub ahead of print]

Monacell JT1, Carbone I.
Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics.
Bioinformatics. 2014 Feb 20. [Epub ahead of print]

Chen ZX, Chen KX, et al.
Multi-algorithm and multi-model based drug target prediction and web server.
Acta Pharmacol Sin. 2014 Feb 3. doi: 10.1038/aps.2013.153. [Epub ahead of print]

Al Mansoori S, Beatson SA, et al.
uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation.
BMC Bioinformatics. 2014 Feb 1;15:36. doi: 10.1186/1471-2105-15-36.

Bach F, Boeva V, et al.
SegAnnDB: interactive web-based genomic segmentation.
Bioinformatics. 2014 Feb 3. [Epub ahead of print]

Agostini F, Bolognesi B, et al.
The cleverSuite Approach for Protein Characterization: Predictions of Structural Properties, Solubility, Chaperone Requirements and RNA-Binding Abilities.
Bioinformatics. 2014 Feb 3. [Epub ahead of print]

Blake JA, Bianchi DW, et al.
DFLAT: functional annotation for human development.
BMC Bioinformatics. 2014 Feb 7;15:45. doi: 10.1186/1471-2105-15-45.

Eren AM, Huse SM, et al.
VAMPS: a website for visualization and analysis of microbial population structures.
BMC Bioinformatics. 2014 Feb 5;15:41. doi: 10.1186/1471-2105-15-41.

Gupta S, Panda B, et al.
SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.
BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40.

Mielke CJ1, Mandarino LJ, Dinu V.
AMASS: a database for investigating protein structures.
Bioinformatics. 2014 Feb 26. [Epub ahead of print]

Burns KH, Halper-Stromberg E, et al.
Visualization and probability-based scoring of structural variants within repetitive sequences.
Bioinformatics. 2014 Feb 21. [Epub ahead of print]

Lao O, Liu F, Wollstein A, Kayser M.
GAGA: A New Algorithm for Genomic Inference of Geographic AncestryReveals Fine Level Population Substructure in Europeans.
PLoS Comput Biol. 2014 Feb 20;10(2):e1003480.

Jia P, Zhao Z.
VarWalker: Personalized Mutation Network Analysis of Putative CancerGenes from Next-Generation Sequencing Data.
PLoS Comput Biol. 2014 Feb 6;10(2):e1003460.

Colwill K, Creixell P, et al.
CoreFlow: A computational platform for integration, analysis and modeling of complex biological data.
J Proteomics. 2014 Feb 3. [Epub ahead of print]

Tuzhikov A, Panchin A, Shestopalov VI.
TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences.
Biotechnoiques 2014 Feb 1;56(2):78-84. doi: 10.2144/000114135.

Hatje K, Kollmar M.
Kassiopeia: a database and web application for the analysis of mutually exclusive exomes of eukaryotes.
BMC Genomics. 2014 Feb 10;15:115. doi: 10.1186/1471-2164-15-115.

Barhdadi A, Dubé MP, et al.
Comparison of genotype clustering tools with rare variants.
BMC Bioinformatics. 2014 Feb 21;15(1):52. [Epub ahead of print]

Du R, Jin L, et al.
Evaluation of copy number variation detection for a SNP array platform.
BMC Bioinformatics. 2014 Feb 21;15(1):50. [Epub ahead of print]

Pullen N, Morris RJ.
Bayesian model comparison and parameter inference in systems biology using nested sampling.
PLoS One. 2014 Feb 11;9(2):e88419. doi: 10.1371/journal.pone.0088419.

Altay G, Kurt Z, Dehmer M, Emmert-Streib F.
Netmes: assessing gene network inference algorithms by network-based measures.
Evol Bioinform Online. 2014 Feb 6;10:1-9. doi: 10.4137/EBO.S13481.

Filed under

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.